QC Resources

Microscope QC publications

Publication	Brief Description
Nature Methods Special Edition: Reporting and reproducibility in Microscopy: https://www.nature.com/nmeth/volumes/18/issues/12	Several papers as output from QUAREP-LiMi, highlighting the requirements for robust image metadata annotation and capture.
Boehm, U., Nelson, G., et al. (2021). QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy. Nature Methods https://doi.org/10.1038/s41592-021-01162-y	Overview White Paper describing QUAREP-LiMi’s work
Nelson, G., Boehm, U., et al. (2021). QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy https://doi.org/10.1111/jmi	A detailed white paper describing the need for QC, and how QUAREP-LiMi is endeavouring to drive this forward.
Confocal ISO 21073:2019, purchasable from the ISO Standards https://www.iso.org/standard/69820.html website, or possibly available via https://bsol.bsigroup.com/ for your Institution, or check https://www.bsigroup.com/en-GB/about-bsi/uk-national-standards-body/Library-Access-to-Standards/ for access.	This ISO covers some basic QC and details how the tests should be performed for Confocal Microscopes. We have added Methods covering these in the Samples and Measurements tab.
Hng KI, Dormann D. ConfocalCheck–a software tool for the automated monitoring of confocal microscope performance. PLoS One. 2013;8(11)	Confocal Check: a image-J-based tool to monitor various aspects of confocal microscope performance.
Cole RW, Jinadasa T, Brown CM. Measuring and interpreting point spread functions to determine confocal microscope resolution and ensure quality control. Nature Protocols volume6, pages1929–1941 (2011)	Outlines a procedure for the collection and interpretation of 3D microsphere measurements using a confocal microscope[link]
Halter M, Bier E, DeRose PC, Cooksey GA, Choquette SJ, Plant AL, Elliott JT. An automated protocol for performance benchmarking a widefield fluorescence microscope. Cytometry A. 2014 Nov;85(11):978-85. PMID: 25132217	[link]
International test results for objective lens quality, resolution, spectral accuracy and spectral separation for confocal laser scanning microscopes. Cole RW¹, Thibault M, Bayles CJ, Eason B, Girard AM, Jinadasa T, Opansky C, Schulz K, Brown CM. Microsc Microanal 2013 Dec;19(6):1653-68.	[link]
Ferrando-May E et.al. German BioImaging network Advanced light microscopy core facilities: Balancing service, science and career. Microsc Res Tech 2016 Jun;79(6):463-79.	Community-led paper (German bioimaging) describing the state of German core imaging facilities, staffing, equipment and maintenance including quality control protocols.[link]

Microscope QC imaging resources & links

PSFJ	Tool to probe microscope performance through analysis of point spread functions obtained from imaging fluorescent beads. Nice comparison of performance metrics obtained from various high NA objectives. [Patrick Theer, Michael Knop, Cyril Mongis]
MetroloJ	Tool to track various aspects of microscope performance: field illumination, PSF, axial resolution & co-alignment. [Fabrice Cordelieres & Cedric Matthews]
MFM Toolbox	Metrology suitcase – QC toolbox that can be shipped to your lab contains QC samples, protocols and instrumentation to allow the end user to calibrate and quality control their microscope [France only, email: metrologie@groupes.renater.fr].
MIPs for PSF	Image J macro to automate the analysis of PSF shape and dimension [Laurent Gelman, Jens Rietdorf link]
NoiSee	ImageJ macro that measures SNR and signal to background ratio of Confocal detectors using either beads or fluorescein solution. Accompanying paper describes a comparison of different detectors (PMT, GaAsP, HyD) across various microscopes.
Daybook2	Commercial software for analysing and collating metrics from the Argolight series of slides, allowing comparison of microscope performance changes over time.

Common QC Tools, Manufacturers and links

PS-Speck beads	175 nm beads in 4 colours throughout the visible spectrum for checking PSF shapes.
Gatta-Quant Nanorulers	Most of their DNA origami based products are aimed at super-resolution microscopy, but these rulers are optimised for confocal resolution at 1AU. They also supply sub-resolution 23 nm ‘beads’ in 1 or 2 colour combinations for checking PSFs.
Argolight HM slide	Etched fluorescent slide that allows one to check multiple microscope parameters such as field homogeneity, apochromaticity, intensity linearity, z drive accuracy, as well as software to compare the results.
PSF-Check slide	Etched fluorescent slide that covers many of the parameters as the Argolight slide above.
Fluorescence reference slides	Homogenous plastic fluorescent slides that allow comparison of field homogeneity and image intensity. Note, these aren’t well suited to multi pinhole systems (eg Spinning disk, iSIM, Airyscan/ SPAD arrays) due to significant crosstalk between pinholes.
Microscope Power sensor	Power sensor in a microscope slide format, allowing easy power reading at the objective focal plane. Supplied by Thorlabs, Excelitas and Argolight.